Chytridiomycosis is caused by Batrachochytrium dendrobatidis (Bd) and contributes significantly to amphibian declines globally. It has affected more than 500 amphibian species on five continents. In South Asia, the Western Ghats is an amphibian biodiversity hotspot; however, the population status of anurans and their burden of chytridiomycosis are not well understood. Our aim was to understand pathogen prevalence, load, and its persistence in a stream anuran community in the Western Ghats. We carried out a capture-mark-recapture (CMR) programme in five ephemeral streams of the Tillari Conservation Reserve (TCR), Western Ghats, India, from 2018 to 2020 during the early (wet) and late (dry) recovery periods. We used quantitative Polymerase Chain Reaction (qPCR) to assign disease states - no (N), low (L), and High (H) levels to every anuran, based on the Bd loads detected. We constructed population models using CMR data from skittering frogs, with Program MARK, and estimated transition probability, apparent survival probability, and capture probability in each disease state. We found that the overall Bd prevalence was 74.6% in the community, with an average infection load of 49 to 700 zoospores/swab. Many anurans cleared infections between early (wet) and late (dry) recovery periods, while some maintained high infection loads. In skittering frogs, the infection states did not influence capture probabilities and apparent survival probabilities. The transition probability between infection states was random, and transitions from any disease state to low were more probable than transitions from any disease state to high or no disease states. The maintenance of a substantial burden of Bd in the anuran community with no apparent impact on their survival or capture probabilities suggests an effective pathogen transmission mechanism. As anurans continue to show a declining trend in the Asian tropics, investigation on the impacts of sub-clinical Bd infections in anurans needs impetus.